To obtain differentially expressed gene sets (DEG; genes which are significantly more or less expressed in a given tissue compared to others) for each of 53 tissue type, the normalized expression (zero mean of log2(RPKM+1)) is used. Two-sided Student’s t-tests are performed per gene per tissue against all other tissues. After the Bonferroni correction, genes with corrected P-value < 0.05 and absolute log fold change ≥ 0.58 are defined as a DEG set in a given tissue, i.e., for these gene expression in the given tissue had the largest discrepancy with expression in all other tissues. In addition, we distinguish between genes that are upregulated and downregulated in a specific tissue compared to other tissues, by taking the sign of t-score into account. In GENE2FUNC, genes are tested against those DEG sets by hypergeometric tests to evaluate if the prioritized genes (or a list of genes of interest) are overrepresented in DEG sets in specific tissue types.
